Fig. 1: seqFISH reveals all major kidney cell types and their locations within the kidney, as well as compositional and spatial changes following AKI.

A Experimental overview: mice were subject to IRI at day 0 to induce AKI. Control and AKI kidneys were collected on day 28, and seqFISH was performed on frozen kidney sections. B Umap depicting all cell types identified using seqFISH. Normal kidney-specific cell types are highlighted and their locations within the nephron are illustrated. DC – dendritic cells; Macroph – macrophages; DCT-CNT – distal convoluted and connecting tubule; Fib – fibroblasts; IC – intercalated cells; Injured PT – injured proximal tubule cells; LOH-TL-C – thin limb of the loop of Henle (comprising cells of the thin descending limb of the loop of Henle of cortical nephrons and the thin ascending limb of the loop of Henle of juxtamedullary nephrons); LOH-TL-JM – thin limb of the loop of Henle of juxtamedullary nephrons; PC – principal cells; Per – pericytes; Podo – podocytes; PT – proximal tubule; PTS1/2/3 – proximal tubule segment 1/2/3; T – T cells; TAL – thick ascending limb of the loop of Henle; Uro – urothelium; Vasc – endothelial cells. C Spatial location of all cell types in one representative control sample. Left - all cell types, right - 10 cell types out of the total 22 that were identified when plotted individually. These cell types span the cortex and medulla, showing that seqFISH analysis captures all major cell types in different areas of the kidney. D Representative field of view outlined in panel (C) showing the cell masks color-coded by cell type (top) and a zoomed-in image showing RNA expression of representative marker genes (bottom). The image is comprised of the sum of the background and DAPI image to illustrate the underlying tissue morphology. E Violin plot showing the normalized expression of marker genes for each cell type. The bar plot shows the relative abundance of each cell type within the control and AKI samples. F Spatial locations of PTS3, Vasc_2, Injured PT, fibroblasts, and macrophages within one representative control (top) and one AKI (bottom) sample.